Gray, Jeffrey J.

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design

Alford, R. F., Leaver-Fay, A., Jeliazkov, J. R., O’Meara, M. J., DiMaio, F. P., Park, H., Shapovalov, M. V., Renfrew, P. D., Mulligan, V. K., Kappel, K., et al. (2017) · Journal of Chemical Theory and Computation

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 1,532

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Leman, J. K., Weitzner, B. D., Lewis, S. M., Adolf-Bryfogle, J., Alam, N., Alford, R. F., Aprahamian, M., Baker, D., Barlow, K. A., Barth, P., et al. (2020) · Nature Methods

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 888

Deep Learning in Protein Structural Modeling and Design

Gao, W., Mahajan, S. P., Sulam, J., & Gray, J. J. (2020) · Patterns

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 227

Antibody structure prediction using interpretable deep learning

Ruffolo, J. A., Sulam, J., & Gray, J. J. (2022) · Patterns

Protein Structure and DynamicsMonoclonal and Polyclonal Antibodies Research

Cited by 216

Efficient flexible backbone protein-protein docking for challenging targets

Marze, N. A., Roy Burman, S. S., Sheffler, W., & Gray, J. J. (2018) · Bioinformatics

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 173

RosettaAntibody: antibody variable region homology modeling server

Sircar, A., Kim, E. T., & Gray, J. J. (2009) · Nucleic Acids Research

Protein Structure and DynamicsMonoclonal and Polyclonal Antibodies Research

Cited by 161

Analysis and modeling of the variable region of camelid single-domain antibodies

Sircar, A., Sanni, K. A., Shi, J., & Gray, J. J. (2011) · The Journal of Immunology

Monoclonal and Polyclonal Antibodies ResearchProtein Structure and Dynamics

Cited by 92

Flexible Protein-Protein Docking with a Multi-Track Iterative Transformer

Chu, L.-S., Ruffolo, J. A., Harmalkar, A., & Gray, J. J. (2023) · Protein Science

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 42

Flexible protein–protein docking with a multitrack iterative transformer

Chu, L., Ruffolo, J. A., Harmalkar, A., & Gray, J. J. (2024) · Protein Science

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 41

Reliable protein-protein docking with AlphaFold, Rosetta, and replica-exchange

Harmalkar, A., Lyskov, S., & Gray, J. J. (2023) · eLife

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 40

Enhancement of antibody thermostability and affinity by computational design in the absence of antigen

Hutchinson, M., Ruffolo, J. A., Haskins, N., Iannotti, M., Vozza, G., Pham, T., Mehzabeen, N., Shandilya, H., Rickert, K., Croasdale-Wood, R., et al. (2023) · mAbs

Monoclonal and Polyclonal Antibodies Researchvaccines and immunoinformatics approaches

Cited by 22

Toward enhancement of antibody thermostability and affinity by computational design in the absence of antigen

Hutchinson, M., Ruffolo, J. A., Haskins, N., Iannotti, M., Vozza, G., Pham, T., Mehzabeen, N., Shandilya, H., Rickert, K., Croasdale-Wood, R., et al. (2024) · mAbs

Monoclonal and Polyclonal Antibodies Researchvaccines and immunoinformatics approaches

Cited by 22

Simultaneous prediction of antibody backbone and side-chain conformations with deep learning

Akpinaroglu, D., Ruffolo, J. A., Mahajan, S. P., & Gray, J. J. (2022) · PLOS ONE

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 21

Hallucinating structure-conditioned antibody libraries for target-specific binders

Mahajan, S. P., Ruffolo, J. A., Frick, R., & Gray, J. J. (2022) · Frontiers in Immunology

Monoclonal and Polyclonal Antibodies Researchvaccines and immunoinformatics approaches

Cited by 20

Flexible backbone assembly and refinement of symmetrical homomeric complexes

Roy Burman, S. S., Yovanno, R. A., & Gray, J. J. (2019) · Structure

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 18

Truncation of the caspase-related subunit (Gpi8p) of Saccharomyces cerevisiae GPI transamidase: Dimerization revealed

Meitzler, J. L., Gray, J. J., & Hendrickson, T. L. (2007) · Archives of Biochemistry and Biophysics

Fungal and yeast genetics researchGlycosylation and Glycoproteins Research

Cited by 18

Induced fit with replica exchange improves protein complex structure prediction

Harmalkar, A., Mahajan, S. P., & Gray, J. J. (2021) · PLoS Computational Biology

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 16

Induced fit with replica exchange improves protein complex structure prediction

Harmalkar, A., Mahajan, S. P., & Gray, J. J. (2022) · PLOS Computational Biology

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 16

Unified Sampling and Ranking for Protein Docking With DFMDock

Chu, L., Sarma, S., Xu, D., & Gray, J. J. (2026) · Proteins: Structure, Function, and Bioinformatics

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 7

Molecular Display of the Animal Meta-Venome for Discovery of Novel Therapeutic Peptides

Hsiao, M.-H., Miao, Y., Liu, Z., Schütze, K., Limjunyawong, N., Chien, D. C.-C., Monteiro, W. D., Chu, L.-S., Morgenlander, W., Jayaraman, S., et al. (2024) · Molecular & Cellular Proteomics

Venomous Animal Envenomation and StudiesHealthcare and Venom Research

Cited by 6

Molecular Display of the Animal Meta-Venome for Discovery of Novel Therapeutic Peptides

Hsiao, M.-H., Miao, Y., Liu, Z., Schütze, K., Limjunyawong, N., Chien, D. C.-C., Monteiro, W. D., Chu, L.-S., Morgenlander, W., Jayaraman, S., et al. (2025) · Molecular & Cellular Proteomics

Venomous Animal Envenomation and StudiesHealthcare and Venom Research

Cited by 5

Advancing membrane-associated protein docking with improved sampling and scoring in Rosetta

Samnata, R., Harmalkar, A., Prathima, P., & Gray, J. J. (2024) · Journal of Chemical Theory and Computation

Protein Structure and DynamicsLipid Membrane Structure and Behavior

Cited by 5

Predictions from deep learning propose substantial protein–carbohydrate interplay

Canner, S. W., Schnaar, R. L., & Gray, J. J. (2026) · Proceedings of the National Academy of Sciences

Machine Learning in BioinformaticsGlycosylation and Glycoproteins Research

Cited by 4

Predictions from Deep Learning Propose Substantial Protein-Carbohydrate Interplay

Canner, S. W., Schnaar, R. L., & Gray, J. J. (2025) · Proceedings of the National Academy of Sciences

Machine Learning in BioinformaticsGlycosylation and Glycoproteins Research

Cited by 4